Methods for the identification of proteins through mass spectrometry have been hitherto developed.
For example, large numbers of methods of using a molecular weight set (mass fingerprinting), methods for retrieving a sequence database using tandem mass spectrometry (MS/MS) data (MS/MS ion search), and methods for obtaining partial sequence information only from MS/MS spectrum information (de novo sequencing) have been developed, and some of them are available as commercially marketed programs (Non-Patent Documents 2 to 6 and 8).
Furthermore, in recent years, attention has been focused on the functions of RNAs that do not encode proteins (non-coding RNAs), and methods for the identification of a RNA through mass spectrometry have been developed.
For example, there has been reported a method of confirming the presence of a digestion product of a certain RNA from a relatively simple RNA mixture, using the signature mass characteristic to the digestion product (Non-Patent Document 1).
Furthermore, there have also been reports on, for example, de novo sequencing of nucleic acids (Non-Patent Document 7).
Furthermore, for example, an apparatus and a method for the identification of a RNA sequence on the genome using the RNA molecular weight (Patent Document 1) have been reported.
Here, in the mass spectrometry of a protein, the amino acid residues that constitute the protein can be divided into a peptide bond part and a side chain part. Among these, a part that undergoes mass change depending on the type or modification of the amino acid residues is the side chain part, and the peptide bond part usually does not undergo mass change.
On the contrary, in RNAs/DNAs, a constituent nucleotide residue is composed of three parts of a phosphorus residue, a ribose (or a deoxyribose), and a base, and from the viewpoint of the mode of modification, the chemical structure of the nucleotide residue is more complicated than that of a protein. Among these, mass change due to modification can occur in both the ribose and the base. Furthermore, by reflecting this structure, the dissociation patterns of MS/MS spectra tend to be susceptible to complication. Furthermore, even between nucleic acids, RNAs and DNAs have different dissociation patterns, so that in an identification method involving a mass spectrometry of RNA/DNA, score allotment is required in accordance with the respective dissociation pathways.
Therefore, the conventional methods for the identification of a protein through mass spectrometry (as described in Non-Patent Documents 2 to 6) are specialized in proteins, and therefore, the conventional methods cannot be applied to RNAs.